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Originally published as Genetics Published Articles Ahead of Print on November 15, 2004.
Genetics, Vol. 169, 1495-1507, March 2005, Copyright © 2005
doi:10.1534/genetics.104.033068
Patterns of Selection on Synonymous and Nonsynonymous Variants in Drosophila miranda
Carolina Bartolomé*,1,
Xulio Maside*,2,
Soojin Yi
,3,
Anna L. Grant* and
Brian Charlesworth*
* Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637-1573
1 Corresponding author: Unidade de Xenética Evolutiva, Instituto de Medicina Legal, Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
E-mail: cbhusson{at}usc.es
We have investigated patterns of within-species polymorphism and between-species divergence for synonymous and nonsynonymous variants at a set of autosomal and X-linked loci of Drosophila miranda. D. pseudoobscura and D. affinis were used for the between-species comparisons. The results suggest the action of purifying selection on nonsynonymous, polymorphic variants. Among synonymous polymorphisms, there is a significant excess of synonymous mutations from preferred to unpreferred codons and of GC to AT mutations. There was no excess of GC to AT mutations among polymorphisms at noncoding sites. This suggests that selection is acting to maintain the use of preferred codons. Indirect evidence suggests that biased gene conversion in favor of GC base pairs may also be operating. The joint intensity of selection and biased gene conversion, in terms of the product of effective population size and the sum of the selection and conversion coefficients, was estimated to be 
0.65.
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